Objective:To investigate the influence of Y chromosome microdeletion and homologous synapsis abnormalities in spermatocytes of male spermatogenesis failure. Methods: Nine cases were recruited in this study,including controls (3 cases),with normal spermatogenesis in their testes;spermatogenesis failure group (3 cases),with spermatogenesis arrest in their testes and without Y microdeletion;and spermatogenesis failure with Y microdeletion group (3 cases). Immunofluorescent staining technology was used to analyze synaptonemal complexes (SC) of spermatocytes. Results: There were 10%,22%,25% gaps presented in testes of controls,spermatogenesis failure group and spermatogenesis failure with Y microdeletion group,respectively. There were significant differences between two spermatogenesis failure groups and controls (10% vs. 22%,P = 0.012;10% vs. 25%,P = 0.014). However,there was no significant difference between two spermatogenesis failure groups. There were 1%,13%,15% splits presented in testes of controls,spermatogenesis failure group and spermatogenesis failure with Y microdeletion group,respectively. There were significant differences between two spermatogenesis failure groups and controls (1% vs. 13%,P = 0.000;1% vs. 15%,P = 0.000). However,there was also no significant difference between two spermatogenesis failure groups. Conclusion: Homologous synapsis abnormalities may play an important factor in spermatogenesis failure. Furthermore,homologous synapsis abnormalities would be more frequent in infertile men with Y chromosome microdeletion.